Job ID = 14520458 SRX = SRX11781038 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:08:51 prefetch.2.10.7: 1) Downloading 'SRR15480981'... 2022-01-15T10:08:51 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:09:15 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:09:16 prefetch.2.10.7: 'SRR15480981' is valid 2022-01-15T10:09:16 prefetch.2.10.7: 1) 'SRR15480981' was downloaded successfully 2022-01-15T10:09:16 prefetch.2.10.7: 'SRR15480981' has 0 unresolved dependencies Read 5754511 spots for SRR15480981/SRR15480981.sra Written 5754511 spots for SRR15480981/SRR15480981.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:47 5754511 reads; of these: 5754511 (100.00%) were paired; of these: 2193619 (38.12%) aligned concordantly 0 times 3030424 (52.66%) aligned concordantly exactly 1 time 530468 (9.22%) aligned concordantly >1 times ---- 2193619 pairs aligned concordantly 0 times; of these: 295832 (13.49%) aligned discordantly 1 time ---- 1897787 pairs aligned 0 times concordantly or discordantly; of these: 3795574 mates make up the pairs; of these: 2567440 (67.64%) aligned 0 times 1055924 (27.82%) aligned exactly 1 time 172210 (4.54%) aligned >1 times 77.69% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 660221 / 3815007 = 0.1731 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:20:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 19:20:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:20:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:20:53: 1000000 INFO @ Sat, 15 Jan 2022 19:20:58: 2000000 INFO @ Sat, 15 Jan 2022 19:21:04: 3000000 INFO @ Sat, 15 Jan 2022 19:21:10: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:21:16: 5000000 INFO @ Sat, 15 Jan 2022 19:21:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 19:21:16: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:21:16: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:21:22: 6000000 INFO @ Sat, 15 Jan 2022 19:21:24: 1000000 INFO @ Sat, 15 Jan 2022 19:21:28: 7000000 INFO @ Sat, 15 Jan 2022 19:21:31: 2000000 INFO @ Sat, 15 Jan 2022 19:21:32: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:21:32: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:21:32: #1 total tags in treatment: 2976511 INFO @ Sat, 15 Jan 2022 19:21:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:21:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:21:32: #1 tags after filtering in treatment: 1106562 INFO @ Sat, 15 Jan 2022 19:21:32: #1 Redundant rate of treatment: 0.63 INFO @ Sat, 15 Jan 2022 19:21:32: #1 finished! INFO @ Sat, 15 Jan 2022 19:21:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:21:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:21:33: #2 number of paired peaks: 386 WARNING @ Sat, 15 Jan 2022 19:21:33: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sat, 15 Jan 2022 19:21:33: start model_add_line... INFO @ Sat, 15 Jan 2022 19:21:33: start X-correlation... INFO @ Sat, 15 Jan 2022 19:21:33: end of X-cor INFO @ Sat, 15 Jan 2022 19:21:33: #2 finished! INFO @ Sat, 15 Jan 2022 19:21:33: #2 predicted fragment length is 123 bps INFO @ Sat, 15 Jan 2022 19:21:33: #2 alternative fragment length(s) may be 0,123 bps INFO @ Sat, 15 Jan 2022 19:21:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.05_model.r WARNING @ Sat, 15 Jan 2022 19:21:33: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:21:33: #2 You may need to consider one of the other alternative d(s): 0,123 WARNING @ Sat, 15 Jan 2022 19:21:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 19:21:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:21:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:21:36: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:21:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:21:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:21:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.05_summits.bed INFO @ Sat, 15 Jan 2022 19:21:37: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (287 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:21:37: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:21:44: 4000000 INFO @ Sat, 15 Jan 2022 19:21:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 19:21:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:21:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:21:52: 5000000 INFO @ Sat, 15 Jan 2022 19:21:54: 1000000 INFO @ Sat, 15 Jan 2022 19:21:59: 6000000 INFO @ Sat, 15 Jan 2022 19:22:02: 2000000 INFO @ Sat, 15 Jan 2022 19:22:05: 7000000 INFO @ Sat, 15 Jan 2022 19:22:09: 3000000 INFO @ Sat, 15 Jan 2022 19:22:10: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:22:10: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:22:10: #1 total tags in treatment: 2976511 INFO @ Sat, 15 Jan 2022 19:22:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:22:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:22:10: #1 tags after filtering in treatment: 1106562 INFO @ Sat, 15 Jan 2022 19:22:10: #1 Redundant rate of treatment: 0.63 INFO @ Sat, 15 Jan 2022 19:22:10: #1 finished! INFO @ Sat, 15 Jan 2022 19:22:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:22:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:22:10: #2 number of paired peaks: 386 WARNING @ Sat, 15 Jan 2022 19:22:10: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sat, 15 Jan 2022 19:22:10: start model_add_line... INFO @ Sat, 15 Jan 2022 19:22:10: start X-correlation... INFO @ Sat, 15 Jan 2022 19:22:11: end of X-cor INFO @ Sat, 15 Jan 2022 19:22:11: #2 finished! INFO @ Sat, 15 Jan 2022 19:22:11: #2 predicted fragment length is 123 bps INFO @ Sat, 15 Jan 2022 19:22:11: #2 alternative fragment length(s) may be 0,123 bps INFO @ Sat, 15 Jan 2022 19:22:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.10_model.r WARNING @ Sat, 15 Jan 2022 19:22:11: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:22:11: #2 You may need to consider one of the other alternative d(s): 0,123 WARNING @ Sat, 15 Jan 2022 19:22:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 19:22:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:22:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:22:14: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:22:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:22:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:22:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.10_summits.bed INFO @ Sat, 15 Jan 2022 19:22:15: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:22:17: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:22:25: 5000000 INFO @ Sat, 15 Jan 2022 19:22:33: 6000000 INFO @ Sat, 15 Jan 2022 19:22:40: 7000000 INFO @ Sat, 15 Jan 2022 19:22:45: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:22:45: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:22:45: #1 total tags in treatment: 2976511 INFO @ Sat, 15 Jan 2022 19:22:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:22:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:22:45: #1 tags after filtering in treatment: 1106562 INFO @ Sat, 15 Jan 2022 19:22:45: #1 Redundant rate of treatment: 0.63 INFO @ Sat, 15 Jan 2022 19:22:45: #1 finished! INFO @ Sat, 15 Jan 2022 19:22:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:22:45: #2 number of paired peaks: 386 WARNING @ Sat, 15 Jan 2022 19:22:45: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sat, 15 Jan 2022 19:22:45: start model_add_line... INFO @ Sat, 15 Jan 2022 19:22:45: start X-correlation... INFO @ Sat, 15 Jan 2022 19:22:45: end of X-cor INFO @ Sat, 15 Jan 2022 19:22:45: #2 finished! INFO @ Sat, 15 Jan 2022 19:22:45: #2 predicted fragment length is 123 bps INFO @ Sat, 15 Jan 2022 19:22:45: #2 alternative fragment length(s) may be 0,123 bps INFO @ Sat, 15 Jan 2022 19:22:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.20_model.r WARNING @ Sat, 15 Jan 2022 19:22:45: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:22:45: #2 You may need to consider one of the other alternative d(s): 0,123 WARNING @ Sat, 15 Jan 2022 19:22:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 19:22:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:22:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:22:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:22:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:22:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:22:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781038/SRX11781038.20_summits.bed INFO @ Sat, 15 Jan 2022 19:22:49: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (65 records, 4 fields): 2 millis CompletedMACS2peakCalling